Package: methylCC 1.27.0

Stephanie C. Hicks

methylCC: Estimate the cell composition of whole blood in DNA methylation samples

A tool to estimate the cell composition of DNA methylation whole blood sample measured on any platform technology (microarray and sequencing).

Authors:Stephanie C. Hicks [aut, cre], Rafael Irizarry [aut]

methylCC_1.27.0.tar.gz
methylCC_1.27.0.zip(r-4.7)methylCC_1.27.0.zip(r-4.6)methylCC_1.27.0.zip(r-4.5)
methylCC_1.27.0.tgz(r-4.6-any)methylCC_1.27.0.tgz(r-4.5-any)
methylCC_1.27.0.tar.gz(r-4.7-any)methylCC_1.27.0.tar.gz(r-4.6-any)
methylCC_1.27.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
methylCC/json (API)

# Install 'methylCC' in R:

install.packages('methylCC', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/stephaniehicks/methylcc/issues

Datasets:

FlowSorted.Blood.450k.sub - A reduced size of the FlowSorted.Blood.450k dataset
offMethRegions - Unmethylated regions for all celltypes
onMethRegions - Methylated regions for all celltypes

On BioConductor:methylCC-1.27.0(bioc 3.24)methylCC-1.26.0(bioc 3.23)

microarray sequencing dnamethylation methylationarray methylseq wholegenome

6.66 score 18 stars 21 scripts 2 mentions 2 exports 151 dependencies

Last updated from:5f22bd3b6b. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time	Files	Syslog
bioc-checks	NOTE	380
linux-devel-x86_64	OK	717
source / vignettes	OK	619
linux-release-x86_64	OK	685
macos-release-arm64	OK	467
macos-oldrel-arm64	OK	383
windows-devel	OK	514
windows-release	OK	595
windows-oldrel	OK	482
wasm-release	OK	317

Exports:cell_counts estimatecc

Dependencies:abind annotate AnnotationDbi askpass assorthead base64 beachmat beanplot BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocParallel Biostrings bit bit64 bitops blob BSgenome bsseq bumphunter cachem cigarillo cli clipr codetools cpp11 crayon curl data.table DBI dbplyr DelayedArray DelayedMatrixStats digest dir.expiry doRNG dplyr farver fastmap filelock FlowSorted.Blood.450k foreach formatR futile.logger futile.options genefilter generics GenomicAlignments GenomicFeatures GenomicRanges GEOquery glue gtools h5mread HDF5Array hms httr httr2 IlluminaHumanMethylation450kanno.ilmn12.hg19 IlluminaHumanMethylation450kmanifest illuminaio IRanges iterators jsonlite KEGGREST labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise mime minfi multtest nlme nor1mix openssl permute pillar pkgconfig plyr png preprocessCore prettyunits progress purrr quadprog R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RCurl readr rentrez reshape restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rngtools Rsamtools RSQLite rtracklayer rvest S4Arrays S4Vectors scales scrime selectr Seqinfo siggenes snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tzdb utf8 vctrs viridisLite vroom withr XML xml2 xtable XVector yaml

The methylCC user's guide

Introduction | Getting Started | Data | Whole Blood Illumina 450k Microarray Data Example | Using the estimatecc() function | Input for estimatecc() | Running estimatecc() | Compare to minfi::estimateCellCounts() | SessionInfo

Rendered frommethylCC.Rmdusingknitr::rmarkdown

Last update: 2020-03-17
Started: 2019-10-05

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Extract raw data	.extract_raw_data
Finding differentially methylated regions	.find_dmrs
.initialize_theta	.initialize_theta
.initializeMLEs	.initializeMLEs
.methylcc_engine	.methylcc_engine
Expectation step	.methylcc_estep
Maximization step	.methylcc_mstep
Pick target positions	.pick_target_positions
.preprocess_estimatecc	.preprocess_estimatecc
.splitit	.splitit
Helper function to take the product of Z and cell composition estimates	.WFun
Generic function that returns the cell composition estimates	cell_counts cell_counts,estimatecc-method
Estimate cell composition from DNAm data	estimatecc
the estimatecc class	estimatecc-class
A reduced size of the FlowSorted.Blood.450k dataset	FlowSorted.Blood.450k.sub
Unmethylated regions for all celltypes	offMethRegions
Methylated regions for all celltypes	onMethRegions

Usage by other packages (reverse dependencies)